From d3a453a18473a93c205d52aa68cfb2f033f593c1 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Mon, 28 Jul 2014 11:50:02 +0200
Subject: [PATCH] Add cutadapt statistics output to flexiprep runs
---
.../scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala | 6 +++++-
.../nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala | 6 ++++++
2 files changed, 11 insertions(+), 1 deletion(-)
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
index 17df80bf4..2760ead88 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
@@ -19,6 +19,9 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
@Output(doc = "Output fastq file")
var fastq_output: File = _
+ @Output(doc = "Output statistics file")
+ var stats_output: File = _
+
executable = config("exe", default = "cutadapt")
override def versionCommand = executable + " --version"
override val versionRegex = """(.*)""".r
@@ -49,7 +52,8 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
optional("-M", opt_maximum_length) +
// input / output
required(fastq_input) +
- " > " + required(fastq_output)
+ required("--output", fastq_output) +
+ " > " + required(stats_output)
} else {
analysisName = getClass.getSimpleName + "-ln"
"ln -sf " +
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 38b9809da..bb1e004de 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -128,13 +128,19 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
var R2: File = new File(R2_in)
if (!skipClip) { // Adapter clipping
+
val cutadapt_R1 = new Cutadapt(this)
+
if (!skipTrim || paired) cutadapt_R1.isIntermediate = true
cutadapt_R1.fastq_input = R1
cutadapt_R1.fastq_output = swapExt(outDir, R1, R1_ext, ".clip" + R1_ext)
+ cutadapt_R1.stats_output = swapExt(outDir, R1, R1_ext, ".clip.stats")
+
if (outputFiles.contains("contams_R1")) cutadapt_R1.contams_file = outputFiles("contams_R1")
+
add(cutadapt_R1)
R1 = cutadapt_R1.fastq_output
+
if (paired) {
val cutadapt_R2 = new Cutadapt(this)
if (!skipTrim || paired) cutadapt_R2.isIntermediate = true
--
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